Nope. GRBs only last a few minutes, which means they only irradiate one
hemisphere of a planet. The resulting ecological catastrophe might be a
problem for primitives like us, but anyone who can plant a colony in another
solar system is obviously capable of building completely closed life-support
systems. Also, anything that is buried to a decent depth would be unharmed
even on the facing hemisphere (so mines, military command centers, subsea
bases and other such facilities would escape the destruction).

Besides, charting nearby explosive hazards (supernovae, GRB precursors, and
so forth) would seem to be a basic safety measure for such a civilization.
Unless you are going to propose a really unusual explanation for GRBs, we
should expect our E.T.s to know about the hazard before it actually happens.
With fairly modest preperations they can weather the whole thing with
minimal (<10%) casualties.